Changeset 3690e4 for src/Jobs/WindowGrid_converter.cpp

Timestamp:

Feb 2, 2016, 5:50:29 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

9ae11c

Parents:

d1831e (diff), 62d092 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1

File:

• src/Jobs/WindowGrid_converter.cpp (modified) (7 diffs)

src/Jobs/WindowGrid_converter.cpp

@@ -50 +50 @@
 
 #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "Jobs/ChargeSmearer.hpp"
 
 void WindowGrid_converter::addGridOntoWindow(
@@ -178 +179 @@
     const SamplingGrid &grid,
     const double prefactor,
-    const bool OpenBoundaryConditions)
+    const bool OpenBoundaryConditions,
+    const bool DoSmearCharges)
 {
 #ifndef NDEBUG
@@ -244 +246 @@
   }
 
+  /// reset grid to zero everywhere
+
   VMG::Grid::iterator griditer = window.Iterators().Local().Begin();
 //  griditer.advance(pre_offset[0]*total[1]*total[2]);
+  for(N[0]=0; N[0] < total[0]; ++N[0])
+    for(N[1]=0; N[1] < total[1]; ++N[1])
+      for(N[2]=0; N[2] < total[2]; ++N[2]) {
+        ASSERT( griditer != window.Iterators().Local().End(),
+            "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
+        window(*griditer++) = 0.;
+      }
+
+#ifndef NDEBUG
+  ASSERT( griditer == window.Iterators().Local().End(),
+      "InterfaceVMGJob::addWindowOntoGrid() - griditer is not at end of window.");
+#endif
+
+  /// then apply charges onto grid
+
+  griditer = window.Iterators().Local().Begin();
+  SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
+  const ChargeSmearer &smearer = ChargeSmearer::getInstance();
+  // NOTE: GridIterator::operator+=()'s implementation in vmg is broken. DON'T USE!
+//  griditer += pre_offset[0] * total[1] * total[2];
   for(N[0]=0; N[0] < pre_offset[0]; ++N[0])
     for(N[1]=0; N[1] < total[1]; ++N[1])
@@ -251 +275 @@
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
-      }
-  SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
+        griditer++;
+      }
   for(N[0]=0; N[0] < length[0]; ++N[0]) {
-//    griditer.advance(pre_offset[1]*total[2]);
+//    griditer += pre_offset[1] * total[2];
       for(N[1]=0; N[1] < pre_offset[1]; ++N[1])
         for(N[2]=0; N[2] < total[2]; ++N[2]) {
           ASSERT( griditer != window.Iterators().Local().End(),
               "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-          window(*griditer++) = 0.;
+          griditer++;
         }
     for(N[1]=0; N[1] < length[1]; ++N[1]) {
-//      griditer.advance(pre_offset[2]);
-      for(N[2]=0; N[2] < pre_offset[2]; ++N[2])
-        window(*griditer++) = 0.;
+//      griditer += pre_offset[2];
+      for(N[2]=0; N[2] < pre_offset[2]; ++N[2]) {
+        griditer++;
+      }
+
       for(N[2]=0; N[2] < length[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
@@ -271 +296 @@
         ASSERT( copyiter != grid.sampled_grid.end(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) += prefactor*(*copyiter++);
-      }
-//      griditer.advance(post_offset[2]);
+        // either smear out charges or not.
+        if (DoSmearCharges) {
+          smearer(window, griditer++, prefactor*(*copyiter++));
+        } else {
+          window(*griditer++) += prefactor*(*copyiter++);
+        }
+      }
+//      griditer += post_offset[2];
       for(N[2]=0; N[2] < post_offset[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
+        griditer++;
       }
     }
-//    griditer.advance(post_offset[1]*total[2]);
+//    griditer += post_offset[1] * total[2];
     for(N[1]=0; N[1] < post_offset[1]; ++N[1])
       for(N[2]=0; N[2] < total[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
-      }
-  }
-  //  griditer.advance(post_offset[0]*total[1]*total[2]);
+        griditer++;
+      }
+  }
+//  griditer += post_offset[0] * total[1] * total[2];
   for(N[0]=0; N[0] < post_offset[0]; ++N[0])
     for(N[1]=0; N[1] < total[1]; ++N[1])
@@ -294 +324 @@
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
+        griditer++;
       }
 #ifndef NDEBUG
@@ -302 +332 @@
       "InterfaceVMGJob::addWindowOntoGrid() - copyiter is not at end of window.");
 #endif
-//  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
+
+  //  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
 }